Sounds to me like it might have been the mating surface on the stub axle that was at fault rather than the discs themselves?
I can't remember why, but I removed my discs about 15 years ago and when I replaced them I had a dreadful pulsing through the brake pedal as if the discs were warped. Double-checked the mounting and somehow I'd managed to trap a tiny bit of debris between the disc and stub axle mounting faces. Cleaned them up and flatted them off with a bit of emery cloth and some engineer's blue, reassembled and they've been perfect ever since.
